A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

Expanding the clinical phenotype of individuals with a 3-bp in-frame deletion of the NF1 gene (c.2970_2972del): an update of genotype–phenotype correlation

Purpose: Neurofibromatosis type 1 (NF1) is characterized by a highly variable clinical presentation, but almost all NF1-affected adults present with cutaneous and/or subcutaneous neurofibromas. Exceptions are individuals heterozygous for the NF1 in-frame deletion, c.2970_2972del (p.Met992del), associated with a mild phenotype without any externally visible tumors. Methods: A total of 135 individuals from 103 unrelated families, all carrying the constitutional NF1 p.Met992del pathogenic variant and clinically assessed using the same standardized phenotypic checklist form, were included in this study. Results: None of the individuals had externally visible plexiform or histopathologically confirmed cutaneous or subcutaneous neurofibromas. We did not identify any complications, such as symptomatic optic pathway gliomas (OPGs) or symptomatic spinal neurofibromas; however, 4.8% of individuals had nonoptic brain tumors, mostly low-grade and asymptomatic, and 38.8% had cognitive impairment/learning disabilities. In an individual with the NF1 constitutional c.2970_2972del and three astrocytomas, we provided proof that all were NF1-associated tumors given loss of heterozygosity at three intragenic NF1 microsatellite markers and c.2970_297

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Waiting time distribution of generalized later patterns

In this paper the concept of later waiting time distributions for patterns in multi-state trials is generalized to cover a collection of compound patterns that must all be counted pattern-specific numbers of times, and a practical method is given to compute the generalized distribution. The solution given applies to overlapping counting and two types of non-overlapping counting, and the underlying sequences are assumed to be Markovian of a general order. Patterns are allowed to be weighted so that an occurrence is counted multiple times, and patterns may be completely included in longer patterns. Probabilities are computed through an auxiliary Markov chain. As the state space associated with the auxiliary chain can be quite large if its setup is handled in a naïve fashion, an algorithm is given for generating a "minimal" state space that leaves out states that can never be reached. For the case of overlapping counting, a formula that relates probabilities for intersections of events to probabilities for unions of subsets of the events is also used, so that the distribution is also computed in terms of probabilities for competing patterns. A detailed example is given to illustrate the methodology.

Effect of water on the glass transition of a potassium-magnesium carbonate melt

Calorimetric measurements of the glass transition temperatures (Tg) of hydrous carbonate melts are reported on a near-eutectic composition of 55 mol% K2CO3 - 45 mol% MgCO3 with up to 42 mol% bulk H2O dissolved in the carbonate melt. Hydrous melts were quenched from 750°C to transparent and crystal-free glasses and were subsequently analysed for water content before and after measuring Tg by high-sensitivity differential scanning calorimetry. The glass transition and limited fictive temperatures as a function of the water content were determined at 10 K/min cooling/heating rates resulting in Tg ranging from 245°C at nominally anhydrous conditions to 83°C in the presence of 42 mol% H2O in the glass. Through a generalized Gordon-Taylor analysis, the factors k (7.27), k0 (3.2) and the interaction parameter Ax (0.49) were derived. The limited fictive temperature of a hypothetically, zero water containing 55 mol% K2CO3 - 45 mol% MgCO3 glass is 232 ± 5°C (505 K). The high value of the interaction parameter A indicates strong specific molecular interactions between water and the carbonates in the glassy state and a large decrease in the excess enthalpy of mixing during the conversion of the glassy into the liquid state at the glass transition. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 1)'.ISSN:1364-503XISSN:1471-296

Glass transition temperatures and crystallization kinetics of a synthetic, anhydrous, amorphous calcium-magnesium carbonate

We report the first calorimetric observations of glass transition temperatures and crystallization rates of anhydrous, amorphous calcium-magnesium carbonate using fast scanning differential scanning calorimetry. Hydrous amorphous Ca0.95Mg0.05CO3 · 0.5H2O (ACMC) solid was precipitated from a MgCl2-NaHCO3 buffered solution, separated from the supernatant, and freeze-dried. An aliquot of the freeze-dried samples was additionally dried at 250°C for up to 6 h in a furnace and in a high-purity N2 atmosphere to produce anhydrous ACMC. The glass transition temperature of the anhydrous Ca0.95Mg0.05CO3 was determined by applying different heating rates (1000-6000 K s-1) and correcting for thermal lag to be 376°C and the relaxational heat capacity was determined to be Cp = 0.16 J/(g K). Additionally, the heating rate dependence of the temperature that is associated with the corrected crystallization peaks is used to determine the activation energy of crystallization to be 275 kJ mol-1. A high-resolution transmission electron microscopy study on the hydrous and anhydrous samples provided further constraints on their compositional and structural states. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 1)'.ISSN:1364-503XISSN:1471-296

Fracture fixation in the operative management of hip fractures (FAITH): an international, multicentre, randomised controlled trial

Background Reoperation rates are high after surgery for hip fractures. We investigated the effect of a sliding hip screw versus cancellous screws on the risk of reoperation and other key outcomes. Methods For this international, multicentre, allocation concealed randomised controlled trial, we enrolled patients aged 50 years or older with a low-energy hip fracture requiring fracture fixation from 81 clinical centres in eight countries. Patients were assigned by minimisation with a centralised computer system to receive a single large-diameter screw with a side-plate (sliding hip screw) or the present standard of care, multiple small-diameter cancellous screws. Surgeons and patients were not blinded but the data analyst, while doing the analyses, remained blinded to treatment groups. The primary outcome was hip reoperation within 24 months after initial surgery to promote fracture healing, relieve pain, treat infection, or improve function. Analyses followed the intention-to-treat principle. This study was registered with ClinicalTrials.gov, number NCT00761813. Findings Between Mar